April 23, 2011

Re-thinking Mendeley

I've got a blog post I'd like to finish here, but it needs time for me to sit down and write it properly. One of the things that has eaten my time instead is looking over Mendeley. In the past I haven't used it because I haven't had a need for it. I already have accounts on Zotero, CiteULike and I have a copy of Papers for my PDFs. I think this could change as I've been working with Mendeley accounts for AoBBlog.

If you visit AoBBlog you'll see a Bibliographies option on the menu bar, and dropping down from that four options. Three of these are shared collections and Pollination is curated by David Frost, the managing editor of the Annals of Botany. These are all administered at Mendeley. I've set up Arabidopsis, Ecology and Nutrition as shared collections so that when people who know more about Arabidopsis etc. than me sign up, they can keep the bibliography up-to-date. The reason you can see it on the website and not have to guess which AoB staff member is keeping the collection on Mendeley is that Mendeley now has an API, allowing me to pull data out of the site. There's also a WordPress plugin for Mendeley and that's how I've been able to put something quickly on the web rather than try to delve into JSON myself.
So why care?

About a year ago I put together a list of archaeology articles in PLoS ONE for someone. Recently Martin Rundkvist has also had a look at Archaeology in PLoS ONE. Now if I'd thought to make the PLoS papers I'd found a collection, then I could create a page for the bibliography, or else just drop it in below. Being able to add papers to Mendeley with one click and using the API would mean that you'd be getting the latest version whenever you visited the page, rather than the mid-2010 version. Handling shared collections is a bit more problematic at the moment, but in the near future a small group of people could make their references public on a collaborative project.
There are some problems. The API is new, and it's not possible to pull all the data out of Mendeley yet. Page numbers are the most obvious missing data. There's also a limited query rate, 150 queries an hour. This may rise in the future but for now it means you'll have to cache results. It's awkward but it's not inherently a bad thing. Cached data are usually much faster, and it's not like references will need much updating once they're in a cache. A paper isn't going to cease being published in Antiquity in 2003 and be published in AJA 2005, unless you've entered the data incorrectly. Tags and related papers are the attributes that are most likely to change and even these could often be updated on a weekly or monthly basis.
I'll concede merely listing papers, even if it's an automatically updated list, might not sound that exciting, so try this.
WordPress allows you to set up custom content types, and one of those types could be references. When the API is fully working you'll be able to use it to populate you database with references from Mendeley. Mendeley in turn works with Zotero and CiteULike, so you could use these services to update your WordPress bibliographic database through Mendeley. Additionally these references need not be yours, they could be your contacts so you're getting help from your personal research network. You can then write a plugin that will work using shortcodes so you can include references in posts or pages in a format like [ref-JonesH2009a]. The plugin formats the short code into the reference style that you want and includes the bibliography formatted in the right style at the bottom of the post. Then you can use Anthologize to render it into the format you want. It could turn WordPress into a social academic research environment. To take it further, you can make the blog private for members for collaborative research, or practice open research, however you want to do it. All of this would be accessible from anywhere with an internet connection.
It's not possible yet, but it could be less than a year away. Personally, I think a tool where I can write drafts and which can ask me "Have you considered these additional papers?" when I add a citation would be extremely useful.
As a reality check I don't yet have the skills with JSON or AJAX to write all of such a plugin myself but it's not beyond my ability to learn given enough time.